Thank you frozenjoy. With FastQ on galaxy I need to trim the first three letters for my record to be able use the barcode splitting function. I haven't tried the stand-alone version yet. I will give that a go once I can get it to work on my computer.
These three letters are important for my analysis, so I am not entirely sure if I can use FastX's barcode splitter tool. I am playing around with the galaxy version of it at present.

then you should be able to prefix your barcodes w/ 3 N's as long as you set --mismatches to at least 3 on the command line when running the script.

One caveat is that you will want to toss out any reads that have any Ns in the first X bases (where X = 3+ barcode length). Have you run FastQC? If so, this will tell you the per base N content. It probably won't be an issue if you've already done preliminary filtering based on Illumina's Y/N flags (assuming Illumina sequencing, of course).

Also, (depending on your computer, of course) I suspect fastx_barcode_splitter.pl will run a lot faster at the CLI than on Galaxy (at least if you are using the public galaxy server).

Edit: to avoid the potential problem w/ Ns, just use some other non-nucleotide character!

Thank you frozenwithjoy. I should give this a go too. We are thinking about running our own Galaxy server in the EC2, so the revised fastx_barcode_splitter might come in handy. Browseruk's script below works super fast, I am not sure how fastx_barcode_splitter.pl might compare.